Variables in the analysis were: days to the first postoperative RSA examination, alignment of the stem, postoperative CCD angle, change in CCD angle and offset, categorized distance (0 2, 2 4, 4 6, > 6 mm) to the medial and lateral cortex, the amount of femoral neck resection, and the occurrence of stress shielding (steady-state migration only).
Intriguingly, examination of alignment data for the cysteine-rich metal-binding domain alone reveals that in a subset of species, mainly protozoa, sequences with a corresponding pattern of cysteines are found as tandem repeats, and lacking the helical domain.
Manual examination of alignments showed that such indels occur not only as extensions to pre-existing structures, but are introduced in existing domains into the middle of the structure.
Sequences with 10% or more undetermined bases or chimeric features, as determined by screening with MALLARD [10] followed by manual examination of alignments generated by BLAST against GenBank, were removed.
Examination of alignments of the full-length proteins revealed 10 fully conserved residues (R112, G129, N131, R147, G151, E153, N164, Y166, G211, D213 where the numbers refer to the alignment positions in Fig. S2); all were located within the β-domain.
This was checked by manual examination of alignments.
The examination of alignments of reads in the clusters for potential alternative splicing identified different splice variants in ca. 9% of the contigs containing reads from more than 1 cDNA insert, or ca. 3% of all genes examined.
Closer examination of alignments using reference sequences from the IMGT/HLA database and the IGV browser showed that the MIT-NGS calls were correct rather than the original SBT results.
These 10 protein coding gene regions were aligned by eye to the dataset used in Near et al. [ 40] and confirmed by examination of alignments of the inferred amino acid sequences.
Direct visual examination of edited alignment was also carried out to minimize the risk of alignment error.
Examination of the alignment found two sub-populations of sequences that did not fit the overall alignment consensus in these regions (Table S2).
